SOMNiBUS
This package is for version 3.19 of Bioconductor; for the stable, up-to-date release version, see SOMNiBUS.
Smooth modeling of bisulfite sequencing
Bioconductor version: 3.19
This package aims to analyse count-based methylation data on predefined genomic regions, such as those obtained by targeted sequencing, and thus to identify differentially methylated regions (DMRs) that are associated with phenotypes or traits. The method is built a rich flexible model that allows for the effects, on the methylation levels, of multiple covariates to vary smoothly along genomic regions. At the same time, this method also allows for sequencing errors and can adjust for variability in cell type mixture.
Author: Kaiqiong Zhao [aut], Kathleen Klein [cre], Audrey Lemaçon [ctb, ctr], Simon Laurin-Lemay [ctb, ctr], My Intelligent Machines Inc. [ctr], Celia Greenwood [ths, aut]
Maintainer: Kathleen Klein <kathleen.klein at mail.mcgill.ca>
citation("SOMNiBUS")):
Installation
To install this package, start R (version "4.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("SOMNiBUS")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("SOMNiBUS")| Analyzing Targeted Bisulfite Sequencing data with SOMNiBUS | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | DNAMethylation, DifferentialMethylation, Epigenetics, FunctionalPrediction, Regression, Sequencing, Software |
| Version | 1.12.0 |
| In Bioconductor since | BioC 3.13 (R-4.1) (3.5 years) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.1.0) |
| Imports | Matrix, mgcv, stats, VGAM, IRanges, GenomeInfoDb, GenomicRanges, rtracklayer, S4Vectors, BiocManager, annotatr, yaml, utils, bsseq, reshape2, data.table, ggplot2, tidyr |
| System Requirements | |
| URL | https://github.com/kaiqiong/SOMNiBUS |
| Bug Reports | https://github.com/kaiqiong/SOMNiBUS/issues |
See More
| Suggests | BiocStyle, covr, devtools, dplyr, knitr, magick, rmarkdown, testthat, TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | SOMNiBUS_1.12.0.tar.gz |
| Windows Binary (x86_64) | SOMNiBUS_1.12.0.zip |
| macOS Binary (x86_64) | SOMNiBUS_1.12.0.tgz |
| macOS Binary (arm64) | SOMNiBUS_1.12.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/SOMNiBUS |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/SOMNiBUS |
| Bioc Package Browser | https://code.bioconductor.org/browse/SOMNiBUS/ |
| Package Short Url | https://bioconductor.org/packages/SOMNiBUS/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.19 | Source Archive |